SMTL ID : 8dm6.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, F.368 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.339 Hydrogen bonds: A:D.336, A:D.336 NAG.2: 3 residues within 4Å: Chain B: N.36, E.40, Q.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.38, B:Q.323 NAG.3: 3 residues within 4Å: Chain B: K.9, N.73, T.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.75 NAG.4: 4 residues within 4Å: Chain B: Q.64, Q.84, N.86, H.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.86 NAG.5: 2 residues within 4Å: Chain B: N.305, M.306 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: F.268, N.415, W.577 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.268 NAG.7: 2 residues within 4Å: Chain B: S.403, N.529 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.403, B:S.403, B:S.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-02-08

Peptides

Spike glycoprotein: A
Processed angiotensin-converting enzyme 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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